Aim Ecological connectivity is currently considered to be essential to enhance biodiversity conservation efforts and benefit adjacent areas. We evaluate the spatial structure of vulnerable marine benthic invertebrate populations based on connectivity to improve the placement of marine protected areas. Location Gulf of Lions, NW Mediterranean Sea. Methods We used a spatially explicit metapopulation model to explore how larval dispersal affects marine benthic invertebrate dynamics at local and regional scales. Minimum recruitment success (the proportion of larvae that settle in a site and survive between spawning and first reproduction, which is required to ensure species persistence) is proposed as a measure of vulnerability. Three contrasting simulations were constructed: closed versus connected populations, habitat loss versus recruitment failure disturbances and varying patterns of oceanographic connectivity. The rescue factor (the ratio of minimum recruitment success in connected and closed populations) quantified the decrease in vulnerability because of oceanographic connectivity. Results In the Gulf of Lions, connectivity reduced population vulnerability by a rescue factor of 5.3. The minimum recruitment success for regional persistence decreased from 3% to 0.2% when species' life expectancies increased from 2 to 50 years. Connectivity enabled the spread of individuals over the entire region, but there were higher densities in sink sites, where low retention rates do not allow for local persistence (western tip of the gulf). Source sites, defined as those sites bringing metapopulation resistance to recruitment failure and stresses from habitat loss, were located in the centre of the gulf. Main conclusions Connectivity drives the spatial structure of population density distribution and population vulnerability in the absence of any other structuring factor. In the Gulf of Lions, marine protected areas are located in population sinks; however; if protection measures were taken in the central part, populations would benefit throughout the region via the rescue effect.